WARNING: SPOILERS AHEAD
Tangentially related to exos, have you thought about allowing motherships to spawn during the final "push" of the spire campaign once you complete it?
Think about the epic showdown of 8 super-dreadnoughts vs. 5 motherships, plus a whole bunch of other stuff.
Now I understood that you disabled motherships during the "triumphant push" for a few reasons. One, to ensure that the spire would win. Two, to not make it an instant loss if the AI makes it to you before the Spire can take out both AIs. And Three, because of their core shield gen properties.
To deal with one, careful tuning of the mothership spawn rate would take care of that. So long as the mothership's spawn rate (adjusted for firepower and durability) is less than the spire spawn rate (adjusted for firepower and durability), the Spire will eventually win. (Basically, make it such that once both start spawning, the number of motherships spawned over a time T does not overpower the number of super-dreadnuaghts + dreadnaughts spawned over time T) This may be a tricky ratio to find, but it would be epic.
Do deal with three, you can make a separate version of the mothership that does not have CSG properties, but is otherwise identical, and have that spawn during the "final push"
Not sure what to do about two though.